I don't think it has as much to do with the software you're creating it in as much as the production method. If you are truly seeking to "layer vinyl" then you must work in vectors and you must think in terms of positive shapes and holes in those shapes that allow underlying layers to show through.
Layered vinyl is inherently superior for longevity over printed vinyl graphics but they are more expensive to produce and install.
Have you looked at
the tutorial put together by GraphiXtreme?